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2 Answers
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As I commented earlier, I am pretty sure that much of these alternations are due to phonological rules. I realized that, among your patterns, a/e-alternation and u/i-alternation follow naturally from assuming:

However, this does not explain your o/i-alternation and a/o-alternation. This fact suggest two possibilities: (1) the underlying verb is of somewhat different quality, and assuming an appropriate underlying vowel, these alternation actually fit the rule mentioned in 2, or (2) there is another rule in addition to the one mentioned in (2).

To the extent that this theory is correct, it predicts that there can be o/e-alternation such that in compound forms, ends with [o], and in isolated forms, ends with [e].

1) I don't think that you have missed anything or that you should really be concerned about it too much. Even without exhaustive research, people who know a lot about kanji know that these readings stand out as being special. Perhaps one of the readings is used in two, rather than just one word, but the sound would still seem unique in comparison to the variety of words used with the other readings. So, I hope my 90%-sure "yes" can set your mind at ease?

2) This link goes directly to a page with a list of kanji with readings that appear exclusively in one word.

3) Are words like this still being created? Yes. To what extent? That's a more difficult question. People are still doing it quite often for names, and I imagine it happens with some frequency as new words are created to describe things (e.g., in science). It's hard to quantify, especially because I wasn't able to uncover a list of 'new words' in Japanese. 日本語の新しい言葉/日本語のつぐに作った言葉とか.... These google keywords don't turn much up, but I'll try to be more creative for your cause and do a little more searching.... Anyway, I hope it's sufficient to say 'it's not a dead practice'.

It seems to me, the reason people use these "distinct" readings is because they're easier to say. I think some strange English sentences are thought of in the same way. You can tell by saying tongue twisters. They force your cheeks to go in-and-out, or your tongue to thrash to-and-fro in such a meticulous manner. For strange English sentences, saying them normally has the same effect. In Japanese, try saying "MOkuNOha", then "KInoHA", and then try saying "konoHA". The upper-case indicate open cheeks, and the lower-case indicate closed cheeks. It's easier to move your cheeks from in to out, rather than out, to in, to out, to in, so I think we just elect this simple variation.

I do not think that the original form of このは (木の葉) is もくのは.
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Tsuyoshi ItoAug 11 '11 at 18:17

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Your reply does not seem to be relevant to my comment. Your answer suggests that きのは was derived from もくのは because the former was easier to pronounce. That is false.
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Tsuyoshi ItoAug 13 '11 at 12:56

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(1) I do not know what you are talking about. I cannot edit or delete your comment because I am not a moderator. (2) Obviously, pronunciation is not the only reason why some form is used and other forms are not. I do not think that このは was chosen over もくのは because of pronunciation, and I think that your comparison between このは and もくのは is irrelevant.
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Tsuyoshi ItoAug 14 '11 at 11:42

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“Anyone can edit anyone's answer.” So what? You were talking about comments, and now you are talking about answers.
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Tsuyoshi ItoAug 14 '11 at 12:27

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From your own comments: “I suggested that konoha was used rather than kinoha or mokunoha because it's easier to pronounce.” “I don't think that konoha was chosen over mokunoha because of pronunciation, […]” You seem to have a difficulty keeping your opinion consistent.
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Tsuyoshi ItoAug 14 '11 at 12:30